bohdan-khomtchouk Goto Github PK

adv-r-book-solutions

Solutions for the Advanced R Development book

agebioportal

R Shiny web application for aging-related diseases

ar-prototype

biochat

Natural language processing of Gene Expression Omnibus data

biosemble

AI assembly of bioNLP wordnets

bohdan-khomtchouk.github.io

Bohdan Khomtchouk's personal website

book-errata-community-service

My contributions towards improving modern machine learning literature

c_from_python

Succinct way to call C from Python

cardioinformatics

Cardioinformatics: the nexus of bioinformatics and precision cardiology

codon-usage

Machine learning scripts/analyses to accompany manuscript entitled "Codon usage bias levels predict taxonomic identity and genetic composition" (for code re-use/reproducibility purposes)

differential-expression-scripts

Miscellaneous differential gene expression scripts in R

encode_histone_genextender_analysis

geneXtendeR analysis on 198 human histone modification ChIP-seq ENCODE datasets

encode_tf_genextender_analysis

geneXtendeR analysis on 547 ENCODE ChIP-seq datasets for both proximal and distal transcription factor (TF) binding peaks for all cell types

fastheatmap

Super high performance interactive heatmap software

flowsom-rtsne-example

Worked example showing how to cluster and visualize flow/mass cytometry data using FlowSOM and Rtsne

ftpwalker

PyPI package for traversing extremely large FTP directory trees

gaussian-distributed-codon-frequencies-of-genomes

Source code to accompany manuscript entitled "Gaussian-distributed codon frequencies of genomes" (Khomtchouk & Nonner, 2019)

genespark

geneSpark is a bioinformatics software program written in Python and Apache Spark for big data epigenetic histone modification ChIP-seq analysis.

genextender

R/Bioconductor package for optimized functional annotation of ChIP-seq data

gtf

R package to provide gene transfer format files from commonly investigated model organisms in ChIP-seq studies

happybirthday

Calculate upcoming birthday dates of Github repos

heatmapgenerator

Cross-platform GUI desktop application for making biological heatmaps

jarvis

kmh-dbgap-utils

Some helpers for dealing with dbgap xmls

linkscraper

R web scraper download utility for links on HTML pages

memor

rmarkdown template that supports customizable logo, company info, etc.

microscope

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

moviescenegiffer

An automated and more advanced and quick way of generating movie gifs

nero-nlp

NERO-nlp is a PyPI package for biomedical Named Entity (Recognition) Ontology

ngstoolkit

One-stop shop for one-click NGS analyses from the command-line